And so it Begins
by DoctorWhoofFanFics
Summary: The beginning of the end has arrived, and with it the arrival of the Pony Who is Not... Their life as they know it is being shattered, and soon time will meet the same fate.
1. Chapter 1

**This is a brand new series, I've sorta given up with the dr. whoof one because since the new episodes aired, they kinda screwed up what I had in mind for the story, so instead i will be trying to work on this one.**

**The Big Reveal**

The citizens of Ponyville slept soundly in the dark midst of the cold wintery night. Snow fell softly to the ground, and all that could be heard was silence, broken only by the soft ring of a bell, signaling midnight. All was peaceful and well here in Ponyville, however, that was soon going to change….

***The Royal Canterlot Castle***

"Luna, what day is it?" asked a tall white pony with feathery wings and a large horn.

"Day 11, year 1003 of our rule, 'Tia." responded Princess Luna, another alicorn similar to Celestia, aside from being smaller with a dark blue color scheme.

"I see. Then it has begun, sister… The arrival of him… of the 'pony who is not'…. And wherever he goes, trouble shall always follow. "

***The following morning***

"Good morning, Spike! We've got a long day ahead of us, first we have to re-organize all the books in the library, then we need to double check that all the books are in the correct order, then triple check that we double checked correctly, then we have to….", listed a violet pony rather excitedly.

"Twilight! It's too early! Can't I just get a few more hours of sleep?" whined a purple and green dragon.

"Okay Spike, but that means you won't be able to come help Rarity with making her new dress!" teased Twilight Sparkle.

"Rarity? I'm up, I'm up! C'mon Twilight, let's get going!" exclaimed Spike as he zipped from his bed to the bathroom.

"Always works." Twilight said as she giggled to herself.

***11:04AM***

"…Stay right there Twilight, I'm almost done your new dress!" demanded a white mare with a purple mane, as she headed off to another room.

"This wasn't what I had in mind when she said that she needed help with a dress…" mumbled Twilight. She looked at her dragon companion, who had a few stitching needles sticking from his scales. "Ummm Spike? Doesn't that hurt?" she asked, a bit concerned.

"Nah, I put on fake scales. Can't feel a thing, though there is no pain that would keep me from assisting _Rarity_" he finished dreamily.

"Oh Twilight, what do you think would suit you better? Emeralds or rubies?" asked Rarity from inside the boutique.

"Oh sister…" sighed Twilight.

"Your right, what was I thinking? Emeralds or rubies… Sapphires are the way to go!" answered Rarity.

Twilight glanced at the room Rarity was still in, and back to Spike. The young dragon was in some sort of trance, daydreaming about something she wasn't sure she wanted to know about. Guessing no other pony was looking, she silently crept out of boutique and into the quiet streets of Ponyville. Twilight breathed out in relief, and looked around. It was quiet, with the exception of a large ticking clock tower. Taking a glance at the time, it read 11:10. Just as she was about to walk away from the boutique, the clock ticked ahead by a minute, and to her surprise, it began to ring.

"What? Why would a clock start ringing now?" she wonder aloud, returning her glare to the clock. It read 11:11AM, so she was unsure why it had rang. "Maybe it was a mistake…" she thought. Suddenly, the sky began to shake. The purple unicorn looked into the sky with wide eyes, as a tiny crack opened up. A bright light began falling from the sky, shaking and twirling crudely in the air. She watched in alarm as the object smashed right near the public library, her home. She galloped at full speed towards the large tree, astounded at what stood before her: A large blue box, with the words 'POLICE BOX' written on the top.

"What in the name of Celestia?" said the confused mare. Curiosity got the better of the pony, and she approached the fallen object and reached out with her hoof, touching the wooden doors. To her surprise, they began opening…


	2. Chapter 2

**Who Now?**

A light brown colt with ragged clothing tumbled from the box, and smashed right into the purple pony. "Blimey! That's never happened before!" said the mysterious colt, as he shook off some snow from his mane. "Hmm… let's see… Hooves… four… muzzle, tattoo, bowtie… wait… something's not right… I don't have a bowtie on! The hooves might be a problem too… Oh, what's this? A tail?" continued the colt, as he yanked on the hair underneath him.

"OW!" exclaimed Twilight in pain. "That's MY tail!" she said, before pushing him off her.

"Oh, sorry, my bad!" apologized the newcomer, helping the downed mare to her hooves. "Now, if you'd excuse me, I have to find a mirror." Said the colt, as he dashed towards the Everfree Forest.

"Well… that was weird…" said Twilight, as she began towards the blue box.

"Uhm, excuse me, sorry to bother you again, but would you-"

"AH!" screamed the startled mare, who was surprised by the sudden reappearance of the colt.

"Just me again! Anyways, I was wondering if you would happen to know where I can find a mirror? Or anything reflect-y?"

"Errr… sure… I have one in my house, follow me" Twilight responded hesitantly.

The two ponies entered the nearby library, to which Twilight showed the strange colt to a full sized mirror.

"Well… let's see… Hooves… mane… tail… It appears I'm a pony! That's strange…"

"Errr Hmm" Twilight interrupted. "Who are you? I don't think I've seen a pony like you before in town."

"I'm not quite sure… I think I'm still me… I don't remember regenerating, so I must still be me…as a pony…"

"Uhh… come again?"

"Sorry, sorry, always bad with introductions! I'm the Doctor! Pleased to meet you, Miss…?"

"Twilight Sparkle. So, what were you doing in that box anyways? And why did it fall out of the sky? Don't tell me you're _another_ banished royal pony?"

"No, at least I don't think so. Anyways, I'm a traveler, and that box is my transportation. Or at least was, unless I learn how to fly with my mouth, because I don't think these can do much." The Doctor complained, gesturing to his hooves. "Well, I'll figure that out later, first things first, I need a bowtie!"

* * *

><p>"Finished!" declared Rarity, as she stepped out with a tweed jacket and a bowtie. "Here you are, sir!" she said, as she proudly handed the outfit to the Doctor.<p>

"Thank you, my dear!" said the Doctor happily, as he quickly began putting on his new clothing, twirling around after he finished. "What do you think?" he said, as he adjusted his bowtie.

"The jacket fits fine, but the bowtie…" criticed Rarity.

"Oi! Bowties are cool!"

"I see… Twilight, your new friend is… how should I put this? A fashion cry for help! But, not for long, I have so many new design ideas in mind for him! So where did you meet him?"

"I guess you could say he sort of 'dropped in'" replied Twilight, while struggling to remove the new sapphire covered dress that Rarity had so 'generously' made her. "So, Doctor, you were telling me where you came from?"

"Oh, come on, Sparkle, let's not dwell on the boring stuff! New look, new planet, let's have a looksee!"

"But I'm from here-hey! Wait up!" said Twilight as she ran out the door after the Doctor, as Rarity looked on.

"He's a strange pony, but he seems nice. Spike? We're heading out now, would you care to join us?" asked Rarity, who ventured into the next room. "Oh!" giggled Rarity, as Spike laid tangled with threads, lying asleep on the floor. "Sweet dreams, Spikey-Wikey" said Rarity sweetly, as she quietly exited the room and the boutique with a scarf and boots. "Now, where in Ponyville did those two wander off to?"

* * *

><p>In the darkest corner of Equestria, where no light has touched or ever will, three minds stirred.<p>

_Is it time…? _One thought.

_Yes brother, the time has come to repay the Princess for imprisoning us here… _Responded another.

_SILENCE, FOALS. We are not yet ready to confront her… we have yet to grow strong enough. Our victory will come, in time, but not so hastily. We will make her suffer for her actions… We will target those close to her, destroy her from the inside out. _Declared the final mind.

_But how? We have already done so to her sister, even her land and people through that dragonesque. Surely there is nothing else dear to her?_

_ There is but one… her prized pupil… the bearer of Magic._

_ Yes… she is weak. Through her suffering and demise, our vengeance will be all the sweeter… Even Time itself will shatter after we are done…_

* * *

><p>"Flying ponies controlling the weather? And I thought the Medusa Cascade was impressive!" commented the Doctor, as he looked into the cloudy skies. A trial of rainbows erupted from the clouds, and zoomed through them, creating a gap within the clouds. The rainbow trial continued the process a few more times, until the clouds and the snow had all disappeared.<p>

"Ha! That's got to be a new record!" declared the blue Pegasus.

"Hey Rainbow Dash! Over here!" yelled Twilight.

"Huh? Oh, heya Twilight!" Rainbow greeted, descending to the ground. "Who's your friend over there?"

"Hello, I'm the Doctor!" replied the Doctor.

"I'm Rainbow Dash, the greatest flier in all of Equestria! Yes, yes, you're honored by my presence".

"Come now, Rainbow Dash, it is very unladylike to gloat." Disapproved Rarity.

"Fine…buzzkill" muttered the Pegasus. "So, Doc, what's wrong with flying ponies controlling the weather? Never seen a Pegasus before?"

"Actually… no."

The three mares stared at him in surprise.

"What, are you from another planet or something?" joked Rainbow.

"Yes." Replied the Doctor.

An uneasy silence spread across the three mares, which was broken at last by the arrival of a bubbly pink earth pony.

"Hey girls! What are you all doing standing out here? Ooh Ooh! Are we having a standing contest? I just love games! Can I pla- *Gasp* !" stopped the pink pony. She quickly ran into a nearby building marked with the sign 'Sugarcube Corner'.

"What just happened…?" wondered the Doctor out loud.

"Oh, just Pinkie Pie bein' Pinkie Pie. Looks you you're getting a party, Doc!" explained Rainbow Dash.

**Second Chapter, sorry it's sort of boring, but had to get some of the introductions out of the way. Next up, a little surprise from the party pony!**


	3. Chapter 3

**Plain Sight**

"I told you I look good in a hat!" said the Doctor smugly, wearing a ridiculous party hat provided by the pink party pony herself.

"So, were you surprised? Were you? Were you? Huh, huh, huh? See I threw this party just for you because I never seen you before, and I know every pony in Ponyville so if I've never seen you before then that means you must be new in town, and if your new in town that means you don't know anypony, and that made me soooo sad, so then I got an idea to throw you this party!" proclaimed Pinkie Pie as fast as she could.

"Hey egghead, it's like your first day all over again!" Said Rainbow Dash playfully. Twilight rolled her eyes with a grin. "So, Doctor, want to meet the rest of the gang?" asked Rainbow.

"Gladly!" exclaimed the Doctor. "Excuse me, my dear." The Doctor said as he passed Pinkie Pie.

"Silly colt, I'm not a deer, I'm a pony!" laughed Pinkie Pie as the Doctor followed Rainbow Dash and Twilight.

They quickly approached a group of three mares chattering among themselves.

"Hey girls I'd like you to meet our new… err… friend, the Doctor!" announced Twilight.

"Pleased ta meetcha, Doc! I'm Applejack!" greeted the orange mare.

"Oh… um… h… hello… I'm Fluttershy…" introduced a yellow mare.

Rarity approached the Doctor and whispered "You must excuse our dear friend, Fluttershy, she's very shy around newcomers such as yourself, though she'll come around once she's warmed up to you."

"I see… well then ponies, now that the introductions are all in order, let's get this party started!" exclaimed the Doctor.

The music began to increase in volume, and soon all ponies were dancing and chattering and enjoying themselves.

"Hahahaha, you're terrible! That is embarrassing!" laughed Twilight as the Doctor danced, which was a spectacle in itself. Arms waving, hooves all over the place, it was indeed an embarrassing site.

"Don'tcha think that's a little strange, comin' from you Twilight?" smirked Applejack.

"I am not that bad!" replied Twilight.

"Um.. Twilight dear, she does have a point…" agreed Rarity hesitantly.

"Seconded" said Rainbow Dash.

Twilight looked at the three mares with an intimidating glare, before breaking into laughter. The Doctor stopped his wild dancing, and proceeded towards a table filled with snacks.

"I can't believe there are jammie dodgers in another universe!" he said surprised. Then he felt something; A shaking feeling. He looked around to see if anyone else noticed. Then he looked towards a bowl of punch. Sure enough, it was vibrating.

"Twitchy twitcha twitchy twitch!" yelled Pinkie Pie.

Suddenly, a powerful tremor struck, sending books and glasses falling from shelves and stands.

"EARTHQUAKE! EVERYPONY GET DOWN!" announced Applejack.

The panicked ponies threw themselves on the floor and under tables and chairs in an attempt to shield themselves from the oncoming debris caused by the quake. The Doctor reached into his pocket and pulled out a strange pen-like device. Pressing a button, the claws at the end extended, and the crystal at the end began glowing and emitting a strange sound.

"That's impossible… This quake is being caused by some sort of… WHOA!" cried the Doctor as another huge tremor hit, knocking the Doctor down…

* * *

><p>"You okay, Doc'?" asked a concerned Applejack. "You sure hit yer head hard".<p>

The Doctor began to awaken, looking dazed for half a second. He immediately propped straight up looking unharmed and well. "Four hooves… muzzle… ears… Still a pony, that's good." He quickly got up and surveyed his surroundings. Most of the other ponies had long left, but the six that he met still remained. "Blimey, that was one heck of a quake! Do you ponies normally get quakes like that?"

"No, not normally", answered Twilight. "Say, what is that thing in your hoof anyways?"

The Doctor looked into his right hoof and noticed he was still holding his sonic screwdriver.

"Oh nothing, just a torch", he answered, pocketing the screwdriver. "How long have I been out?"

"Not sure, the quake lasted for quite a while… but it's night right now. Say, Doctor, where are you staying-"

"Thank you, Twilight! That's very kind of you!" said the Doctor has he began walking off.

"Wait! What?" Twilight said, confused. She turned towards her fellow ponies . "What just happened? Wait, Doctor, I live over there!" she said, as she ran off towards the Doctor, leaving the other five mares with a dumbstruck look on their faces.

"Hey, Pinkie, we should start cleaning up Sugar Cube Corner…" suggested Rainbow Dash.

"Okie Dokie Lokie!" agreed Pinkie Pie.

As the five mares all agreed, they entered the building, unaware that something was watching them…

* * *

><p>"Fine Doctor, but only for <span>one<span> night. Got it?"

"Got it, one night!"

Twilight entered the library and wearily marched upstairs. "Spike?"

"Yeah Twilight?" answered the young dragon.

"The Doctor is staying here tonight, so try not to wake him if you go downstairs?"

"Sure thing Twilight"

The two entered Twilight's room and drifted off to sleep… only to be woken up 10 minutes later. At least one was. Spike was still fast asleep, while Twilight was woken by a wheezing sound. She walked downstairs to see the Doctor, wide awaken, with wires coming from his phone box.

"What are you doing? How did you get that inside here!" questioned Twilight.

"Re-wiring my… phonebox…" answered the Doctor nonchalantly.

"Right… rewiring… a phonebox…" repeated Twilight. She went upstairs and muttered to herself.

"Crazy pony… phonebox… wires…" She jumped in her bed and twisted and turned for a few minutes, before deciding she couldn't sleep. "Maybe some fresh air will help…" she said, as she opened her window a bit. The cool air helped calm her, but she was still wide awake. She glanced outside, hoping for something to distract her a bit. That's when she noticed something strange: a grey pony. She blinked, and when she opened her eyes the pony was gone. Alarmed, she quickly ran downstairs again, only to be greeted with a sleeping Doctor, who was snoring on the couch. Walking quietly, she ventured outside with her boots and scarf, looking for the grey pony.

(_* for a better reading experience, put this after youtube :/watch?v=V5QM-Csxqu8&feature=&t=2m10s)_

"Hello? Is anypony there?" she asked. No response. She looked towards her window, and then back at her spot. This was where she spotted the pony. Twilight looked around the ground, and then noticed some hoofprints. The only problem with these prints, however, was that they led towards her house.

"What…? But…" wide eyed with concern, she looked towards her window once more, only to be met with a shocking site: The grey pony, watching her from her own bedroom. The now scared mare ran towards her house as fast as she could. She turned around to shut the door, only to see another grey pony standing a few feet away.

_A statue…it's a statue…_ the distraught mare thought to herself. She quickly shut the door and ran to her room. Spike was still sleeping, however she saw a trace of rapidly melting snow near her window. Twilight grabbed Spike and flung up over her back, and galloped down into the main room, calling for the Doctor.

"Doctor? What's going on! There's these strange statues…" Twilight stopped. Three statues were surrounding her.

She blinked.

_They look like their coming closer… what's going on! _

She blinked again.

They were literally a foot away now. "Stay back!" she cried, as she slowly inched backwards, before tripping on the couch behind her. She quickly looked up, and saw the statues with hooves lifted towards her, and blood thirsty grins on their faces. With sheer determination, she focused her glare on them for as long as she could.

_DO NOT BLINK. DO NOT BLINK. DO. NOT. BLINK._

Alas, she could not hold out any longer, and her eyes closed… and something grabbed her.


	4. Chapter 4

**Quite A lot of Talking**

"Blimey, Sparkle! I leave for one minute and you've got a horde of weeping angels after you! That's a new record, even for me!

"Doctor…"

"That's strange… these angels resemble ponies… are they from your world? Wait. What world are we in? Evestree… or… Evangee… Equestion?"

"Doctor!..."

"That's doesn't sound right… Another thing I just noticed… some of your pony friends have wings like the statues, but no horn. Is that sort of a removable part or something?

"DOCTOR!"

The Doctor stopped his rambling and looked at his companion.

"Yes?"

"What happened to those… those…" Twilight trailed off.

"Weeping Angels. Yes, yes, they look like stone, like statues, but they're not. It's actually a defense mechanism; they turn to stone when being observed by any sentient being, becoming quantum locked." The Doctor replied, speaking as if the statues were trivial topics.

"B…but… we're not watching them! Why aren't they coming to get us?"

"See for yourself, Ms. Sparkle."

The distraught unicorn looked towards the once active group of angels, only to find them frozen. She blinked, expecting them to move in, though when her eyes reopened the angels remained the same way. She turned her head towards the couch, and realized the mattresses had been torn off, revealing a strange lens-like device.

"What did you do to my couch?"

"I repaired it," grinned the Doctor. "Right now, it's projecting a one-way image visible only to those facing it by manipulating the patterns of light around the area, creating an illusion of multiple sentient beings. That'll keep 'em still for about half an hour."

"So it's like one-way glass with fake reflections?"

"No, it's nothing like that at all, but if it will help you understand, then yes."

Twilight grunted in frustration at his answer. Then she felt a poke on her back. Turning around, she discovered Spike awake and confused.

"Uh… Twilight? How come we're in the living room? And what's with the freaky statues?" the confused dragon asked.

"I'll explain later Spike. First off, Doctor, are they dangerous?"

"Oh yes, quite. Very dangerous, very lethal. Would you like to poke one?"

Facehoofing, the purple unicorn got up and headed for the door. "Come on Doctor, Spike. We've got to warn the others before these statues get to them."

"Right then, let's get going, shall we?"

The three companions left the library in a hurry, towards the bakery.

Running to the door, Twilight pounded on it as fast and as loudly as she could.

"Pinkie Pie! Open up!"

No answer. Twilight proceeded to knock even harder now, worried for her friends.

"Move aside, Sparkle," Said the Doctor, as he produced the torch from earlier. He pointed the device at the door and activated it, creating a whirling sound.

"How are you going to open a door with a - *click*"

"Ladies first, Ms. Twilight," said the Doctor with a grin.

"How did you… never mind," stopped Twilight, as she ran past the Doctor and into the bakery. She took a quick look around, scanning for any signs of either her friends or the angels.

"Where did everypony go?" she wondered aloud.

"Twilight? Is that you?" cried a voice from another room.

"Rarity? Where are you?"

"We're upstairs sugarcube! Come quickly, we're in a heap o' trouble!" replied Applejack.

The unicorn raced upstairs with the Doctor and Spike following shortly. They arrived to see the five mares backed in a corner, surrounded by angels.

"Twilight! Thank Celestia you came when ya did! Ya gotta help us, these things are lookin' fer trouble!" said Applejack.

"Working on it, Applejack! Doctor, you seem to have the most experience here! What do we do?" demanded Twilight.

"Just… Don't blink! I'll think of something…" answered the Doctor.

"Twilight! The door!" cried Rainbow Dash.

The Doctor and Twilight immediately twirled to the door, and standing in the doorway was an angel that was dangerously close.

"No! Our only way out is blocked!" cried Twilight.

"Wait, what about that window over there?" asked Spike.

Fluttershy shook her head. "We already tried, the window is locked. It won't budge."

"Twilight, you and your friends keep your eyes on the angels," commanded the Doctor.

The six mares and Spike trained their glare on the angels, making sure all of them were insight, while the Doctor soniced the window. Lifting hard, the window slid smoothly, presenting a way of escape.

"C'mon everyon- pony! That's gonna need some getting used to… What? Oh, right. C'mon everypony!" Said the Doctor.

The five ponies and Spike jumped out the window, one at a time, leaving only the Doctor and Fluttershy still in the room.

"Come on! We have to go!"

"But… but… I can't!" Fluttershy whimpered, with a shakey voice.

"It's either that or them!" the Doctor stated, pointing towards the angels.

"O…okay… I'll… try…" stammered Fluttershy. She slowly got onto the ledge of the window, closed her eyes, and took a deep breath.

"Here I goOOOOOO- Ooof!" yelled a surprised Fluttershy. She looked up and saw Rainbow Dash holding on to her.

"You know you have wings… right?" asked Rainbow Dash.

"Oh… Right… Sorry, "apologized Fluttershy. "Wait! Where's the Doctor?"

The six ponies looked to see the Doctor still facing the angels, slowly backing up.

"You know, you lot were much scarier when you weren't ponies!" said the Doctor, as he neared the windows. "Not... good…" the Doctor muttered, as the angels were slowly moving in on him.

"Don't…" he said, as he faced a group of angels on his left. "Blink." He quickly turned to face the angels on his right, who were now a few seconds away from him.

"Only one way… this might hurt a bit."

Turning as fast as he could, he ran towards the window and dived through, landing hard in the snow.

"OW... Today is turning out to be one of those days… Any who how do you ponies work with these hooves… nearly impossible! No fingers either… how do you lot eat fish custard? Oh wait, do you actually eat meat? Now… how do I get up…Oh? I got it. Never mind!" said the Doctor, as he rose quickly.

"Now, back to the matter at hand… err… hoof, is everypony alright?"

"We're alright, Doc'. But what were 'em statue thingies? Where'd they come from?" asked Applejack.

"Very good questions, and I'll get to answering them… soon," replied the Doctor, glancing at the window, taking note that the angels had already disappeared.

"You have no idea where they're coming from, do you?" accused Rainbow Dash.

"Well… actually… I… no. But I will. Soon." admitted the Doctor.

"Um, excuse me, Doctor? There's something here I think you should see, "said Rarity.

"Maybe sooner than I thought," added The Doctor.

The Doctor followed the marshmallow-like unicorn and arrived at a large gaping hole, surrounded by a thin layer of snow.

"Hello… what have we here?" commented the Doctor, intrigued. He took out his sonic screwdriver again and began pointing it around the hole.

"Doctor, what in Celestia's mane is that device?" asked Rarity.

"Sonic Screwdriver! Never go anywhere without one," answered the Doctor. He held up the screwdriver and extended its claws and body. "Massive amounts of artron energy coming from here… If I'm right, and I'm always, mostly, am, then this is where those angels should be coming from. The answer to your question, Applejack, is down there." The Doctor got up, and surveyed the assembled ponies and dragon. "Down the dark, scary hole filled with murderous, bloodthirsty statues. I love this place already!" He said, facing the hole once more.

"Well then, everypony, who's afraid of the dark…?"

"…me…" whispered Fluttershy.

"Fluttershy! That was supposed to be a cliffhanger line!" yelled Pinkie Pie.

"Sorry... but did you just break the fourth wall?" asked the Doctor, slightly amused.

Pinkie looked at the Doctor with a dumbfound face and blinked twice. "The fourth whatsit?"

"...Never mind."


End file.
